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Wang H, Ye L, Zhou L, Yu J, Pang B, Zuo D, Gu L, Zhu B, Du X, Wang H. Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline-Alkaline Stress in Sorghum bicolor L. Int J Mol Sci 2023; 24:16831. [PMID: 38069156 PMCID: PMC10706439 DOI: 10.3390/ijms242316831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum to saline-alkaline soil are still ambiguous. In this study, RNA sequencing was carried out to explore the gene expression profiles of sorghum treated with sodium bicarbonate (150 mM, pH = 8.0, treated for 0, 6, 12 and 24 h). The results show that 6045, 5122, 6804, 7978, 8080 and 12,899 differentially expressed genes (DEGs) were detected in shoots and roots after 6, 12 and 24 h treatments, respectively. GO, KEGG and weighted gene co-expression analyses indicate that the DEGs generated by saline-alkaline stress were primarily enriched in plant hormone signal transduction, the MAPK signaling pathway, starch and sucrose metabolism, glutathione metabolism and phenylpropanoid biosynthesis. Key pathway and hub genes (TPP1, WRKY61, YSL1 and NHX7) are mainly related to intracellular ion transport and lignin synthesis. The molecular and physiological regulation processes of saline-alkali-tolerant sorghum are shown by these results, which also provide useful knowledge for improving sorghum yield and quality under saline-alkaline conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (H.W.); (L.Y.); (L.Z.); (J.Y.); (B.P.); (D.Z.); (L.G.); (B.Z.)
| | - Huinan Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (H.W.); (L.Y.); (L.Z.); (J.Y.); (B.P.); (D.Z.); (L.G.); (B.Z.)
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2
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Li Z, Shi L, Lin X, Tang B, Xing M, Zhu H. Genome-Wide Identification and Expression Analysis of Malate Dehydrogenase Gene Family in Sweet Potato and Its Two Diploid Relatives. Int J Mol Sci 2023; 24:16549. [PMID: 38068872 PMCID: PMC10706315 DOI: 10.3390/ijms242316549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato (Ipomoea batatas) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba, respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations.
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Affiliation(s)
| | | | | | | | | | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Z.L.); (L.S.); (X.L.); (B.T.); (M.X.)
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3
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Miszalski Z, Kaszycki P, Śliwa-Cebula M, Kaczmarczyk A, Gieniec M, Supel P, Kornaś A. Plasticity of Plantago lanceolata L. in Adaptation to Extreme Environmental Conditions. Int J Mol Sci 2023; 24:13605. [PMID: 37686411 PMCID: PMC10487448 DOI: 10.3390/ijms241713605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed at characterizing some adaptive changes in Plantago lanceolata L. exposed to harsh conditions of a desert-like environment generating physiological stress of limited water availability and exposure to strong light. It was clearly shown that the plants were capable of adapting their root system and vascular tissues to enable efficient vegetative performance. Soil analyses, as well as nitrogen isotope discrimination data show that P. lanceolata leaves in a desert-like environment had better access to nitrogen (nitrite/nitrate) and were able to fix it efficiently, as compared to the plants growing in the surrounding forest. The arbuscular mycorrhiza was also shown to be well-developed, and this was accompanied by higher bacterial frequency in the root zone, which might further stimulate plant growth. A closer look at the nitrogen content and leaf veins with a higher number of vessels and a greater vessel diameter made it possible to define the changes developed by the plants populating sandy habitats as compared with the vegetation sites located in the nearby forest. A determination of the photosynthesis parameters indicates that the photochemical apparatus in P. lanceolata inhabiting the desert areas adapted slightly to the desert-like environment and the time of day, with some changes of the reaction center (RC) size (photosystem II, PSII), while the plants' photochemical activity was at a similar level. No differences between the two groups of plants were observed in the dissipation of light energy. The exposure of plants to harsh conditions of a desert-like environment increased the water use efficiency (WUE) value in parallel with possible stimulation of the β-carboxylation pathway.
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Affiliation(s)
- Zbigniew Miszalski
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Paweł Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Marta Śliwa-Cebula
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Adriana Kaczmarczyk
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Miron Gieniec
- The W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland; (Z.M.); (A.K.); (M.G.)
| | - Paulina Supel
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. Mickiewicza 21, 31-120 Kraków, Poland; (P.K.); (M.Ś.-C.); (P.S.)
| | - Andrzej Kornaś
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Kraków, Poland
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Pérez-López J, Feria AB, Gandullo J, de la Osa C, Jiménez-Guerrero I, Echevarría C, Monreal JA, García-Mauriño S. Silencing of Sb PPCK1-3 Negatively Affects Development, Stress Responses and Productivity in Sorghum. PLANTS (BASEL, SWITZERLAND) 2023; 12:2426. [PMID: 37446987 DOI: 10.3390/plants12132426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays central roles in photosynthesis, respiration, amino acid synthesis, and seed development. PEPC is regulated by different post-translational modifications. Between them, the phosphorylation by PEPC-kinase (PEPCk) is widely documented. In this work, we simultaneously silenced the three sorghum genes encoding PEPCk (SbPPCK1-3) by RNAi interference, obtaining 12 independent transgenic lines (Ppck1-12 lines), showing different degrees of SbPPCK1-3 silencing. Among them, two T2 homozygous lines (Ppck-2 and Ppck-4) were selected for further evaluation. Expression of SbPPCK1 was reduced by 65% and 83% in Ppck-2 and Ppck-4 illuminated leaves, respectively. Expression of SbPPCK2 was higher in roots and decreased by 50% in Ppck-2 and Ppck-4 in this tissue. Expression of SbPPCK3 was low and highly variable. Despite the incomplete gene silencing, it decreased the degree of phosphorylation of PEPC in illuminated leaves, P-deficient plants, and NaCl-treated plants. Both leaves and seeds of Ppck lines had altered metabolic profiles and a general decrease in amino acid content. In addition, Ppck lines showed delayed flowering, and 20% of Ppck-4 plants did not produce flowers at all. The total amount of seeds was lowered by 50% and 36% in Ppck-2 and Ppck-4 lines, respectively. The quality of seeds was lower in Ppck lines: lower amino acid content, including Lys, and higher phytate content. These data confirm the relevance of the phosphorylation of PEPC in sorghum development, stress responses, yield, and quality of seeds.
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Affiliation(s)
- Jesús Pérez-López
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Ana B Feria
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Jacinto Gandullo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Clara de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Irene Jiménez-Guerrero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - José A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
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5
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Trevisan F, Tiziani R, Hall RD, Cesco S, Mimmo T. δ 13C as a tool for iron and phosphorus deficiency prediction in crops. PLANT DIRECT 2023; 7:e487. [PMID: 36950260 PMCID: PMC10027435 DOI: 10.1002/pld3.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Many studies proposed the use of stable carbon isotope ratio (δ13C) as a predictor of abiotic stresses in plants, considering only drought and nitrogen deficiency without further investigating the impact of other nutrient deficiencies, that is, phosphorus (P) and/or iron (Fe) deficiencies. To fill this knowledge gap, we assessed the δ13C of barley (Hordeum vulgare L.), cucumber (Cucumis sativus L.), maize (Zea mays L.), and tomato (Solanum lycopersicon L.) plants suffering from P, Fe, and combined P/Fe deficiencies during a two-week period using an isotope-ratio mass spectrometer. Simultaneously, plant physiological status was monitored with an infra-red gas analyzer. Results show clear contrasting time-, treatment-, species-, and tissue-specific variations. Furthermore, physiological parameters showed limited correlation with δ13C shifts, highlighting that the plants' δ13C, does not depend solely on photosynthetic carbon isotope fractionation/discrimination (Δ). Hence, the use of δ13C as a predictor is highly discouraged due to its inability to detect and discern different nutrient stresses, especially when combined stresses are present.
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Affiliation(s)
- Fabio Trevisan
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Raphael Tiziani
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Robert D. Hall
- Laboratory of Plant PhysiologyWageningen University & ResearchWageningenThe Netherlands
- Business Unit BioscienceWageningen University & ResearchWageningenThe Netherlands
| | - Stefano Cesco
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
| | - Tanja Mimmo
- Faculty of Science and TechnologyFree University of BolzanoBolzanoItaly
- Competence Centre of Plant HealthFree University of Bozen‐BolzanoBolzanoItaly
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6
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Singh J, Garai S, Das S, Thakur JK, Tripathy BC. Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops. PHOTOSYNTHESIS RESEARCH 2022; 154:233-258. [PMID: 36309625 DOI: 10.1007/s11120-022-00978-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.
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Affiliation(s)
- Jitender Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| | - Sampurna Garai
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Shubhashis Das
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research, New Delhi, 110067, India.
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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7
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Feria AB, Ruíz-Ballesta I, Baena G, Ruíz-López N, Echevarría C, Vidal J. Phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxylase kinase isoenzymes play an important role in the filling and quality of Arabidopsis thaliana seed. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:70-80. [PMID: 36099810 DOI: 10.1016/j.plaphy.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/25/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Three plant-type phosphoenolpyruvate carboxylase (PPC1 to PPC3) and two phosphoenolpyruvate carboxylase kinase (PPCKs: PPCK1 and 2) genes are present in the Arabidopsis thaliana genome. In seeds, all PPC genes were found to be expressed. Examination of individual ppc mutants showed little reduction of PEPC protein and global activity, with the notable exception of PPC2 which represent the most abundant PEPC in dry seeds. Ppc mutants exhibited moderately lower seed parameters (weight, area, yield, germination kinetics) than wild type. In contrast, ppck1-had much altered (decreased) yield. At the molecular level, ppc3-was found to be significantly deficient in global seed nitrogen (nitrate, amino-acids, and soluble protein pools). Also, N-deficiency was much more marked in ppck1-, which exhibited a tremendous loss of 95% and 90% in nitrate and proteins, respectively. The line ppck2-had accumulated amino-acids but lower levels of soluble proteins. Regarding carboxylic acid pools, Krebs cycle intermediates were found to be diminished in all mutants; this was accompanied by a consistent decrease in ATP. Lipids were stable in ppc mutants, however ppck1-seeds accumulated more lipids while ppck2-seeds showed high level of polyunsaturated fatty acid oleic and linolenic (omega 3). Altogether, the results indicate that the complete PEPC and PPCK family are needed for normal C/N metabolism ratio, growth, development, yield and quality of the seed.
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Affiliation(s)
- Ana B Feria
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes Nº 6, 41012, Sevilla, Spain.
| | - Isabel Ruíz-Ballesta
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes Nº 6, 41012, Sevilla, Spain
| | - Guillermo Baena
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes Nº 6, 41012, Sevilla, Spain
| | - Noemí Ruíz-López
- Dpto. de Mejora Genética y Biotecnología, IHSM La Mayora, UMA-CSIC. Av. Louis Pasteur, 49, 29010, Málaga, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes Nº 6, 41012, Sevilla, Spain
| | - Jean Vidal
- Institute of Plant Sciences Paris-Saclay(IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. d'Evry, Univ. Paris-Diderot, Univ. Paris-Saclay, Batiment 630, Rue Noetzlin, 91192, Gif-sur-Yvette cedex, France
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de la Osa C, Pérez‐López J, Feria A, Baena G, Marino D, Coleto I, Pérez‐Montaño F, Gandullo J, Echevarría C, García‐Mauriño S, Monreal JA. Knock-down of phosphoenolpyruvate carboxylase 3 negatively impacts growth, productivity, and responses to salt stress in sorghum (Sorghum bicolor L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:231-249. [PMID: 35488514 PMCID: PMC9539949 DOI: 10.1111/tpj.15789] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a carboxylating enzyme with important roles in plant metabolism. Most studies in C4 plants have focused on photosynthetic PEPC, but less is known about non-photosynthetic PEPC isozymes, especially with respect to their physiological functions. In this work, we analyzed the precise roles of the sorghum (Sorghum bicolor) PPC3 isozyme by the use of knock-down lines with the SbPPC3 gene silenced (Ppc3 lines). Ppc3 plants showed reduced stomatal conductance and plant size, a delay in flowering time, and reduced seed production. In addition, silenced plants accumulated stress indicators such as Asn, citrate, malate, and sucrose in roots and showed higher citrate synthase activity, even in control conditions. Salinity further affected stomatal conductance and yield and had a deeper impact on central metabolism in silenced plants compared to wild type, more notably in roots, with Ppc3 plants showing higher nitrate reductase and NADH-glutamate synthase activity in roots and the accumulation of molecules with a higher N/C ratio. Taken together, our results show that although SbPPC3 is predominantly a root protein, its absence causes deep changes in plant physiology and metabolism in roots and leaves, negatively affecting maximal stomatal opening, growth, productivity, and stress responses in sorghum plants. The consequences of SbPPC3 silencing suggest that this protein, and maybe orthologs in other plants, could be an important target to improve plant growth, productivity, and resistance to salt stress and other stresses where non-photosynthetic PEPCs may be implicated.
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Affiliation(s)
- Clara de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Jesús Pérez‐López
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Ana‐Belén Feria
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Guillermo Baena
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Daniel Marino
- Departamento de Biología Vegetal y Ecología, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU)LeioaSpain
- IkerbasqueBasque Foundation for ScienceBilbaoSpain
| | - Inmaculada Coleto
- Departamento de Biología Vegetal y Ecología, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU)LeioaSpain
| | | | - Jacinto Gandullo
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Cristina Echevarría
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - Sofía García‐Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
| | - José A. Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de BiologíaUniversidad de SevillaSevillaSpain
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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Hurtado-Gaitán E, Sellés-Marchart S, Hartwell J, Martínez-Esteso MJ, Bru-Martínez R. Down-Regulation of Phosphoenolpyruvate Carboxylase Kinase in Grapevine Cell Cultures and Leaves Is Linked to Enhanced Resveratrol Biosynthesis. Biomolecules 2021; 11:1641. [PMID: 34827639 PMCID: PMC8615455 DOI: 10.3390/biom11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
In grapevine, trans-Resveratrol (tR) is produced as a defence mechanism against stress or infection. tR is also considered to be important for human health, which increases its interest to the scientific community. Transcriptomic analysis in grapevine cell cultures treated with the defence response elicitor methyl-β-cyclodextrin (CD) revealed that both copies of PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) were down-regulated significantly. A role for PPCK in the defence response pathway has not been proposed previously. We therefore analysed the control of PPCK transcript levels in grapevine cell cultures and leaves elicited with CD. Moreover, phosphoenolpyruvate carboxylase (PPC), stilbene synthase (STS), and the transcription factors MYB14 and WRKY24, which are involved in the activation of STS transcription, were also analysed by RT-qPCR. The results revealed that under CD elicitation conditions PPCK down-regulation, increased stilbene production and loss of PPC activity occurs in both tissues. Moreover, STS transcripts were co-induced with MYB14 and WRKY24 in cell cultures and leaves. These genes have not previously been reported to respond to CD in grape leaves. Our findings thus support the hypothesis that PPCK is involved in diverting metabolism towards stilbene biosynthesis, both for in vitro cell culture and whole leaves. We thus provide new evidence for PEP being redirected between primary and secondary metabolism to support tR production and the stress response.
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Affiliation(s)
- Elías Hurtado-Gaitán
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Susana Sellés-Marchart
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
| | - Maria José Martínez-Esteso
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
| | - Roque Bru-Martínez
- Plant Proteomics and Functional Genomics Group, Agrochemistry and Biochemistry Department, Faculty of Science, University of Alicante, 03690 Alicante, Spain; (E.H.-G.); (S.S.-M.); (M.J.M.-E.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante ISABIAL-Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO, 03010 Alicante, Spain
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11
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Baena G, Feria AB, Hernández-Huertas L, Gandullo J, Echevarría C, Monreal JA, García-Mauriño S. Genetic and Pharmacological Inhibition of Autophagy increases the Monoubiquitination of Non-Photosynthetic Phospho enolpyruvate Carboxylase. PLANTS 2020; 10:plants10010012. [PMID: 33374865 PMCID: PMC7823769 DOI: 10.3390/plants10010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an enzyme with key roles in carbon and nitrogen metabolisms. The mechanisms that control enzyme stability and turnover are not well known. This paper investigates the degradation of PEPC via selective autophagy, including the role of the monoubiquitination of the enzyme in this process. In Arabidopsis, the genetic inhibition of autophagy increases the amount of monoubiquitinated PEPC in the atg2, atg5, and atg18a lines. The same is observed in nbr1, which is deficient in a protein that recruits monoubiquitinated substrates for selective autophagy. In cultured tobacco cells, the chemical inhibition of the degradation of autophagic substrates increases the quantity of PEPC proteins. When the formation of the autophagosome is blocked with 3-methyladenine (3-MA), monoubiquitinated PEPC accumulates as a result. Finally, pull-down experiments with a truncated version of NBR1 demonstrate the recovery of intact and/or fragmented PEPC in Arabidopsis leaves and roots, as well as cultured tobacco cells. Taken together, the results show that a fraction of PEPC is cleaved via selective autophagy and that the monoubiquitination of the enzyme has a role in its recruitment towards this pathway. Although autophagy seems to be a minor pathway, the results presented here increase the knowledge about the role of monoubiquitination and the regulation of PEPC degradation.
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Moosavi SS, Abdi F, Abdollahi MR, Tahmasebi-Enferadi S, Maleki M. Phenological, morpho-physiological and proteomic responses of Triticum boeoticum to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:95-104. [PMID: 32920225 DOI: 10.1016/j.plaphy.2020.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Drought is the most important abiotic stress limiting wheat production worldwide. Triticum boeoticum, as wild wheat, is a rich gene pool for breeding for drought stress tolerance. In this study, to identify the most drought-tolerant and susceptible genotypes, ten T. boeoticum accessions were evaluated under non-stress and drought-stress conditions for two years. Among the studied traits, water-use efficiency (WUE) was suggested as the most important trait to identify drought-tolerant genotypes. According to the desirable and undesirable areas of the bi-plot, Tb5 and Tb6 genotypes were less and more affected by drought stress, respectively. Therefore, their flag-leaves proteins were used for two-dimensional gel electrophoresis. While, Tb5 contained a high amount of yield, yield components, and WUE, Tb6 had higher levels of water use, phenological related traits, and root related characters. Of the 235 spots found in the studied accessions, 14 spots (11 and 3 spots of Tb5 and Tb6, respectively) were selected for sequencing. Of these 14 spots, 9 and 5 spots were upregulated and downregulated, respectively. The identified proteins were grouped into six functional protein clusters, which were mainly involved in photosynthesis (36%), carbohydrate metabolism (29%), chaperone (7%), oxidation and reduction (7%), lipid metabolism and biological properties of the membrane (7%) and unknown function (14%). We report for the first time that MICP, in the group of lipid metabolism proteins, was significantly changed into wild wheat in response to drought stress. Maybe, the present-identified proteins could play an important role to understand the molecular pathways of wheat drought tolerance. We believe comparing and evaluating the similarity-identified proteins of T. boeoticum with the previously identified proteins of Aegilops tauschii, can provide a new direction to improve wheat tolerance to drought stress.
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Affiliation(s)
- Sayyed Saeed Moosavi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Fatemeh Abdi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Mohammad Reza Abdollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sattar Tahmasebi-Enferadi
- Department of Molecular Plant Biotechnology, Faculty of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
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13
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You L, Zhang J, Li L, Xiao C, Feng X, Chen S, Guo L, Hu H. Involvement of abscisic acid, ABI5, and PPC2 in plant acclimation to low CO2. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4093-4108. [PMID: 32206789 PMCID: PMC7337093 DOI: 10.1093/jxb/eraa148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 05/23/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays a pivotal role in the photosynthetic CO2 fixation of C4 plants. However, the functions of PEPCs in C3 plants are less well characterized, particularly in relation to low atmospheric CO2 levels. Of the four genes encoding PEPC in Arabidopsis, PPC2 is considered as the major leaf PEPC gene. Here we show that the ppc2 mutants suffered a growth arrest when transferred to low atmospheric CO2 conditions, together with decreases in the maximum efficiency of PSII (Fv/Fm) and lower levels of leaf abscisic acid (ABA) and carbohydrates. The application of sucrose, malate, or ABA greatly rescued the growth of ppc2 lines under low CO2 conditions. Metabolite profiling analysis revealed that the levels of glycine and serine were increased in ppc2 leaves, while the abundance of photosynthetic metabolites was decreased under these conditions. The transcript levels of encoding enzymes involved in glycine or serine metabolism was decreased in ppc2 in an ABI5-dependent manner. Like the ppc2 mutants, abi5-1 mutants had lower photosynthetic rates and Fv/Fm compared with the wild type under photorespiratory conditions (i.e. low CO2 availability). However, the growth of these mutants was similar to that of the wild type under non-photorespiratory (low O2) conditions. The constitutive expression of ABI5 prevented the growth arrest of ppc2 lines under low CO2 conditions. These findings demonstrate that PPC2 plays an important role in the acclimation of Arabidopsis plants to low CO2 availability by linking photorespiratory metabolism to primary metabolism, and that this is mediated, at least in part, through ABA- and ABI5-dependent processes.
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Affiliation(s)
- Lei You
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jumei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuanlei Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xinhua Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shaoping Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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14
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Badia MB, Maurino VG, Pavlovic T, Arias CL, Pagani MA, Andreo CS, Saigo M, Drincovich MF, Gerrard Wheeler MC. Loss of function of Arabidopsis NADP-malic enzyme 1 results in enhanced tolerance to aluminum stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:653-665. [PMID: 31626366 DOI: 10.1111/tpj.14571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 09/10/2019] [Accepted: 09/19/2019] [Indexed: 05/29/2023]
Abstract
In acidic soils, aluminum (Al) toxicity is a significant limitation to crop production worldwide. Given its Al-binding capacity, malate allows internal as well as external detoxification strategies to cope with Al stress, but little is known about the metabolic processes involved in this response. Here, we analyzed the relevance of NADP-dependent malic enzyme (NADP-ME), which catalyzes the oxidative decarboxylation of malate, in Al tolerance. Plants lacking NADP-ME1 (nadp-me1) display reduced inhibition of root elongation along Al treatment compared with the wild type (wt). Moreover, wt roots exposed to Al show a drastic decrease in NADP-ME1 transcript levels. Although malate levels in seedlings and root exudates are similar in nadp-me1 and wt, a significant increase in intracellular malate is observed in roots of nadp-me1 after long exposure to Al. The nadp-me1 plants also show a lower H2 O2 content in root apices treated with Al and no inhibition of root elongation when exposed to glutamate, an amino acid implicated in Al signaling. Proteomic studies showed several differentially expressed proteins involved in signal transduction, primary metabolism and protection against biotic and other abiotic stimuli and redox processes in nadp-me1, which may participate directly or indirectly in Al tolerance. The results indicate that NADP-ME1 is involved in adjusting the malate levels in the root apex, and its loss results in an increased content of this organic acid. Furthermore, the results suggest that NADP-ME1 affects signaling processes, such as the generation of reactive oxygen species and those that involve glutamate, which could lead to inhibition of root growth.
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Affiliation(s)
- Mariana Beatriz Badia
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Verónica Graciela Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Tatiana Pavlovic
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Cintia Lucía Arias
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María Ayelén Pagani
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Carlos Santiago Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Mariana Saigo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María Fabiana Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Mariel Claudia Gerrard Wheeler
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
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15
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Xiang G, Ma W, Gao S, Jin Z, Yue Q, Yao Y. Transcriptomic and phosphoproteomic profiling and metabolite analyses reveal the mechanism of NaHCO 3-induced organic acid secretion in grapevine roots. BMC PLANT BIOLOGY 2019; 19:383. [PMID: 31481025 PMCID: PMC6724372 DOI: 10.1186/s12870-019-1990-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Organic acid secretion is a widespread physiological response of plants to alkalinity. However, the characteristics and underlying mechanism of the alkali-induced secretion of organic acids are poorly understood. RESULTS Oxalate was the main organic acid synthesized and secreted in grapevine (a hybrid of Vitis amurensis, V. berlandieri and V. riparia) roots, while acetate synthesis and malate secretion were also promoted under NaHCO3 stress. NaHCO3 stress enhanced the H+ efflux rate of grapevine roots, which is related to the plasma membrane H+-ATPase activity. Transcriptomic profiling revealed that carbohydrate metabolism was the most significantly altered biological process under NaHCO3 stress; a total of seven genes related to organic acid metabolism were significantly altered, including two phosphoenolpyruvate carboxylases and phosphoenolpyruvate carboxylase kinases. Additionally, the expression levels of five ATP-binding cassette transporters, particularly ATP-binding cassette B19, and two Al-activated malate transporter 2 s were substantially upregulated by NaHCO3 stress. Phosphoproteomic profiling demonstrated that the altered phosphoproteins were primarily related to binding, catalytic activity and transporter activity in the context of their molecular functions. The phosphorylation levels of phosphoenolpyruvate carboxylase 3, two plasma membrane H+-ATPases 4 and ATP-binding cassette B19 and pleiotropic drug resistance 12 were significantly increased. Additionally, the inhibition of ethylene synthesis and perception completely blocked NaHCO3-induced organic acid secretion, while the inhibition of indoleacetic acid synthesis reduced NaHCO3-induced organic acid secretion. CONCLUSIONS Our results demonstrated that oxalate was the main organic acid produced under alkali stress and revealed the necessity of ethylene in mediating organic acid secretion. Additionally, we further identified several candidate genes and phosphoproteins responsible for organic acid metabolism and secretion.
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Affiliation(s)
- Guangqing Xiang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Wanyun Ma
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Shiwei Gao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zhongxin Jin
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Qianyu Yue
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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16
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Fukuda M, Nishida S, Kakei Y, Shimada Y, Fujiwara T. Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen. PLANT & CELL PHYSIOLOGY 2019; 60:1961-1973. [PMID: 30892644 DOI: 10.1093/pcp/pcz048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/07/2019] [Indexed: 05/07/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.
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Affiliation(s)
- Makiha Fukuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan
| | - Sho Nishida
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, Japan
| | - Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Vegetable and Floriculture Science, NARO, Tsu, Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan
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17
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Zhao Y, Guo A, Wang Y, Hua J. Evolution of PEPC gene family in Gossypium reveals functional diversification and GhPEPC genes responding to abiotic stresses. Gene 2019; 698:61-71. [PMID: 30825597 DOI: 10.1016/j.gene.2019.02.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 02/10/2019] [Accepted: 02/23/2019] [Indexed: 12/24/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) family genes play important roles in regulating plant growth and abiotic stress response. Based on the sequenced Gossypium genomes, we performed comprehensive analysis of PEPC homolog genes in cotton, which six, six, eleven and ten PEPC genes were identified in Gossypium arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2), respectively. These genes were divided into six subgroups: PEPC-i, PEPC-ii, PEPC-iii, PEPC-iv, PEPC-v and PEPC-vi; PEPC genes in each subgroup displayed conserved gene structure and motifs. Segmental duplication and whole genome duplication (WGD) events yielded the expansion of PEPC genes. Expression assays showed that the duplicated PEPC genes displayed diverse expression patterns, indicating that they experienced functional divergence. Of which, genes in PEPC-iv subgroup played crucial role for substrate distribution in cottonseed. Cis-elements, putative miRNAs and expression analyses showed that GhPEPC homologs might respond to abiotic stresses, expression levels of GhPEPC1 and GhPEPC2/GhPEPC2D genes were larger induced than other GhPEPC genes under cold, heat, salt, and drought stresses, indicating the crucial roles in abiotic stresses response. Present study serves new information to decipher the evolution and function of PEPC genes in Gossypium.
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Affiliation(s)
- Yanpeng Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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18
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Zang X, Geng X, He K, Wang F, Tian X, Xin M, Yao Y, Hu Z, Ni Z, Sun Q, Peng H. Overexpression of the Wheat ( Triticum aestivum L.) TaPEPKR2 Gene Enhances Heat and Dehydration Tolerance in Both Wheat and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1710. [PMID: 30532762 PMCID: PMC6265509 DOI: 10.3389/fpls.2018.01710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/02/2018] [Indexed: 05/06/2023]
Abstract
Wheat (Triticum aestivum L.) yield and quality are adversely affected by heat, drought, or the combination of these two stresses in many regions of the world. A phosphoenolpyruvate carboxylase kinase-related kinase gene, TaPEPKR2, was identified from our previous heat stress-responsive transcriptome analysis of heat susceptible and tolerant wheat cultivars. Based on the wheat cultivar Chinese Spring genome sequence, TaPEPKR2 was mapped to chromosome 5B. Expression analysis revealed that TaPEPKR2 was induced by heat and polyethylene glycol treatment. To analyze the function of TaPEPKR2 in wheat, we transformed it into the wheat cultivar Liaochun10, and observed that the transgenic lines exhibited enhanced heat and dehydration stress tolerance. To examine whether TaPEPKR2 exhibits the same function in dicotyledonous plants, we transformed it into Arabidopsis, and found that its overexpression functionally enhanced tolerance to heat and dehydration stresses. Our results imply that TaPEPKR2 plays an important role in both heat and dehydration stress tolerance, and could be utilized as a candidate gene in transgenic breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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19
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Connell MB, Lee MJY, Li J, Plaxton WC, Jia Z. Structural and biochemical characterization of citrate binding to AtPPC3, a plant-type phosphoenolpyruvate carboxylase from Arabidopsis thaliana. J Struct Biol 2018; 204:507-512. [PMID: 30419358 DOI: 10.1016/j.jsb.2018.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/02/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a tightly regulated cytosolic enzyme situated at a crucial branch point of central plant metabolism. The structure of AtPPC3, a C3 PEPC isozyme of the model plant Arabidopsis thaliana, in complex with the inhibitors aspartate and citrate was solved at 2.2-Å resolution. This represents the first PEPC structure with citrate bound. Aspartate and citrate binding sites are in close proximity (5.1-5.3 Å) and interactions between citrate and specific residues were identified. Citrate functions as a mixed (allosteric) inhibitor as it reduced AtPPC3's Vmax while increasing Km(PEP) values. The PEP saturation data gave an excellent fit to the mixed inhibition model, yielding Ki and Ki' (citrate) values of 9.3 and 42.5 mM, respectively. Citrate and aspartate inhibition of AtPPC3 was non-additive, likely due to their closely positioned binding sites, their similar negative charge, and type of binding residues. Fewer interactions and lower affinity for citrate support its observed weaker inhibition of AtPPC3 relative to aspartate. Citrate does not appear to induce further conformational change beyond aspartate owing to the similar structural mechanism of inhibition. AtPPC3 largely exhibits root-specific expression in Arabidopsis, where it is markedly upregulated during stresses such as excessive salinity or nutritional Pi deprivation that necessitate large increases in anaplerotic PEP carboxylation. The cytosolic citrate concentration of potato tubers suggests that AtPPC3's inhibition by citrate may be physiologically relevant. Our results provide novel insights into the structural basis of allosteric PEPC control and the kinetic effects brought about upon inhibitor binding.
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Affiliation(s)
- Matthew B Connell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Michael J Y Lee
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Jerry Li
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - William C Plaxton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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20
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Wang Y, Stevanato P, Yu L, Zhao H, Sun X, Sun F, Li J, Geng G. The physiological and metabolic changes in sugar beet seedlings under different levels of salt stress. JOURNAL OF PLANT RESEARCH 2017; 130:1079-1093. [PMID: 28711996 DOI: 10.1007/s10265-017-0964-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/08/2017] [Indexed: 05/20/2023]
Abstract
Salinity stress is a major limitation to global crop production. Sugar beet, one of the world's leading sugar crops, has stronger salt tolerant characteristics than other crops. To investigate the response to different levels of salt stress, sugar beet was grown hydroponically under 3 (control), 70, 140, 210 and 280 mM NaCl conditions. We found no differences in dry weight of the aerial part and leaf area between 70 mM NaCl and control conditions, although dry weight of the root and whole plant treated with 70 mM NaCl was lower than control seedlings. As salt concentrations increased, degree of growth arrest became obvious In addition, under salt stress, the highest concentrations of Na+ and Cl- were detected in the tissue of petioles and old leaves. N and K contents in the tissue of leave, petiole and root decreased rapidly with the increase of NaCl concentrations. P content showed an increasing pattern in these tissues. The activities of antioxidant enzymes such as superoxide dismutase, catalase, ascorbate peroxidase and glutathione peroxidase showed increasing patterns with increase in salt concentrations. Moreover, osmoprotectants such as free amino acids and betaine increased in concentration as the external salinity increased. Two organic acids (malate and citrate) involved in tricarboxylic acid (TCA)-cycle exhibited increasing contents under salt stress. Lastly, we found that Rubisco activity was inhibited under salt stress. The activity of NADP-malic enzyme, NADP-malate dehydrogenase and phosphoenolpyruvate carboxylase showed a trend that first increased and then decreased. Their activities were highest with salinity at 140 mM NaCl. Our study has contributed to the understanding of the sugar beet physiological and metabolic response mechanisms under different degrees of salt stress.
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Affiliation(s)
- Yuguang Wang
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Research Institute of Chinese Academy of Agricultural Sciences, Crop Academy of Heilongjiang University, Harbin, 150080, China
- The College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Piergiorgio Stevanato
- DAFNAE, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università degli Studi di Padova, Viale dell'Università 16, Legnaro, Padova, 35020, Italy
| | - Lihua Yu
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China
- Sugar Beet Research Institute of Chinese Academy of Agricultural Sciences, Crop Academy of Heilongjiang University, Harbin, 150080, China
| | - Huijie Zhao
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China
| | - Xuewei Sun
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China
| | - Fei Sun
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China
| | - Jing Li
- The College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Gui Geng
- Key Laboratory of Sugar Beet Genetic Breeding of Heilongjiang Province, Heilongjiang University, Harbin, 150080, China.
- Sugar Beet Research Institute of Chinese Academy of Agricultural Sciences, Crop Academy of Heilongjiang University, Harbin, 150080, China.
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